While population genetic diversity has broad application in species conservation, no studies have examined the community-level consequences of this diversity. We show that population genetic diversity (generated by interspecific hybridization) in a dominant riparian tree affects an arthropod community composed of 207 species. In an experimental garden, plant cross type structured the arthropod community of individual trees, and among stands in the wild, plant genetic diversity accounted for nearly 60% of the variation in arthropod diversity. While previous experimental garden studies have demonstrated the effects of plant genotype on arthropod communities, our study extends these findings from individual trees in an experimental garden to natural stands of cottonwoods where plant population genetic diversity was a significant factor structuring arthropod diversity. These findings argue that the preservation of genetic diversity in a dominant species is far more important than previously realized, and may be particularly important in hybridizing systems.